Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgattttacaaatgcaaccccatcatttttctctgtttagataattatgtgttcataattaaacagagttcgagttttttttaacaggaaagcatactctctctctctctctctctctctctctctctcattgaagcagattgttacttacttgtgaagattctgtctgagggttttcgcgatttgtgtagGGAGAGTGAATCTAATAGGAGAGCACATCGATTACGAGGGTTATTCCGTGCTTCCAATGGCAATTCGCCAAGACACGGTGGTTGCTATCGGTAGGCGAGA

Basic information

species Physcomitrella patens
transcript PP1S89_154V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S89_154V6.3 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA17G03990.1 (Glycine max), 3'ss of exon 1
gtttgattttacaaatgcaaccccatcatttttctctgtttagataattatgtgttcataattaaacagagttcgagttttttttaacaggaaagcatactctctctctctctctctctctc-tctctctctcattgaagcagattgttacttacttgtgaagattctgtctgagggttttcgcgatttgtgtagGGAGAGTGAATCTAATAGGAGAGCACATCGATTACGAGGGTTATTCCGTGCTTCCAATGGCAATTCGCCAAGACACGGTGGTTGCTATCGGTAGGCGAGA
                                                                       |     | | | | ||     ||   | || | ||| | |||||||   |  | |   | | ||   |  |||||   |  |    |||         | |   |||||  |||    ||| ||| ||||||||  | || || |||||||| ||||| || |||||||| ||||| || ||||||||||| ||||||||| | || || ||  | |     ||
------------------------------------------------------------------gttcttctctctctctctcaatttctaaattttctatttctttttctctcttaattgtttagtttttatgataagagattagaatattgcggtgtttcacgattattttggtttctgcg----gtgcagGAAGAGTGAACTTGATTGGGGAGCACATTGATTATGAAGGTTATTCGGTGCTGCCTATGGCAATTCGGCAAGACACGATCGTGGCGATTCGGAAAAATGA

upper sequence: PP1S89_154V6.3 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT3G06580.1 (Arabidopsis thaliana), 3'ss of exon 1
gtttgattttacaaatgcaaccccatcatttttctctg--tttagataattatgtgttcataattaaacagagttcgagttttttttaacaggaaagcatactctctctctctctctctctctc---tctctctctcattgaagcagattgttacttacttgtgaagattctgtctgagggttttcgcgattt-----gtgtagGGAGAGTGAATCTAATAGGAGAGCACATCGATTACGAGGGTTATTCCGTGCTTCCAATGGCAATTCGCCAAGACACGGTGGTTGCTATCGGTAGGCGAGA
       |  | ||   |       | | ||||  |     || ||   |  |    |   |  | ||  |  ||| | || || |    | |   |||   |   | | |   |       ||   |     |||  ||| |   | | | ||  |  ||||||| ||      ||| ||| || |  || |     ||||||| ||||||||||| |||||||||||||| || || || || || || ||| | || ||||| ||||| || || ||  |  | || ||  | |   | ||
------gtaaataatctcgggtttttgaatttttgcaaaaattggaatttcgttgactttgagatgaattggtttctaattattgtatcgatgtctgcaattttggtatttggatgatgacatcagatgatcttctgtttggaattgttggata--tgattgtgaaaatagatggtgaaggtgtttgttatattttgtgtgtagGAAGAGTGAATCTGATAGGAGAGCACATTGACTATGAAGGATACTCAGTGTTGCCGATGGCTATTCGTCAGGATACAATTATAGCGATTCGGAAATGTGA

upper sequence: PP1S89_154V6.3 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ17214 (Selaginella moellendorffii), 3'ss of exon 1
gtttgattttacaaatgcaaccccatcatttttctctgtttagataattatgtgttcataattaaacagagttcgagttttttttaacaggaaagcatactctctctctctctctctctctctctctctctcattgaagcagattgttacttacttgtgaagattctgtctgagggttttcgcgatttgtgtagGGAGAGTGAATCTAATAGGAGAGCACATCGATTACGAGGGTTATTCCGTGCTTCCAATGGCAATTCGCCAAGACACGGTGGTTGCTATCGGTAGGCGAGA
                                                                                                                                | |  ||||           | ||     |     |   |  ||  || |  || ||    || |||  |||||||||| || || ||||||||||||||||| || || || ||||| ||||||||||||||||| |||||  | || || || || ||      
-------------------------------------------------------------------------------------------------------------------------------gttttcttgatatttcgctcgatttgtggattggattggcgattggcggctcccggga---atgcagGTCGAGTGAATCTTATCGGCGAGCACATCGATTACGAAGGCTACTCGGTGCTGCCAATGGCAATTCGCCAGGACACAATTGTCGCGATTGGGAGATCCTC

upper sequence: PP1S89_154V6.3 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ30960 (Selaginella moellendorffii), 3'ss of exon 1
gtttgattttacaaatgcaaccccatcatttttctctgtttagataattatgtgttcataattaaacagagttcgagttttttttaacaggaaagcatactctctctctctctctctctctctctctctctcattgaagcagattgttacttacttgtgaagattctgtctgagggttttcgcgatttgtgtagGGAGAGTGAATCTAATAGGAGAGCACATCGATTACGAGGGTTATTCCGTGCTTCCAATGGCAATTCGCCAAGACACGGTGGTTGCTATCGGTAGGCGAGA
                                                                                                                                | |  ||||           | ||     |     |   |  ||  || |  || ||    || |||  |||||||||| || || ||||||||||||||||| || || || ||||| ||||||||||| ||||| |||||| | || || || || ||      
-------------------------------------------------------------------------------------------------------------------------------gttttcttgatattttgctcgatttgtggattggattggcgattggcggctcccggga---atgcagGTCGAGTGAATCTTATCGGCGAGCACATCGATTACGAAGGCTACTCGGTGCTGCCAATGGCAATCCGCCAGGACACGATTGTCGCGATTGGGAGATCCTC

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|208376956|gb|DC936762.1|DC936762
EST:     GTTCGTGCACCATTATGGCCGTGACCCTGAACTCTTTGCGCGTGCTCCAG                         GGAGAGTGAATCTAATAGGAGAGCACATCGATTACGAGGGTTATTCCGTGC
genomic: GTTCGTGCACCATTATGGCCGTGACCCTGAACTCTTTGCGCGTGCTCCAGgtttgatttt ... atttgtgtagGGAGAGTGAATCTAATAGGAGAGCACATCGATTACGAGGGTTATTCCGTGC
EST: gi|100427974|gb|BY959219.1|BY959219
EST:     GTTCGTGCACCATTATGGCCGTGACCCTGAACTCTTTGCGCGTGCTCCAG                         GGAGAGTGAATCTAATAGGAGAGCACATCGATTACGAGGGTTATTCCGTGC
genomic: GTTCGTGCACCATTATGGCCGTGACCCTGAACTCTTTGCGCGTGCTCCAGgtttgatttt ... atttgtgtagGGAGAGTGAATCTAATAGGAGAGCACATCGATTACGAGGGTTATTCCGTGC
EST: gi|162272815|gb|FC448803.1|FC448803
EST:     GTTCGTGCACCATTATGGCCGTGACCCTGAACTCTTTGCGCGTGCTCCAG                         GGAGAGTGAATCTAATAGGAGAGCACATCGATTACGAGGGTTATTCCGTGC
genomic: GTTCGTGCACCATTATGGCCGTGACCCTGAACTCTTTGCGCGTGCTCCAGgtttgatttt ... atttgtgtagGGAGAGTGAATCTAATAGGAGAGCACATCGATTACGAGGGTTATTCCGTGC
EST: gi|208363621|gb|DC935330.1|DC935330
EST:     GTTCGTGCACCATTATGGCCGTGACCCTGAACTCTTTGCGCGTGCTCCAG                         GGAGAGTGAATCTAATAGGAGAGCACATCGATTACGAGGGTTATTCCGTGC
genomic: GTTCGTGCACCATTATGGCCGTGACCCTGAACTCTTTGCGCGTGCTCCAGgtttgatttt ... atttgtgtagGGAGAGTGAATCTAATAGGAGAGCACATCGATTACGAGGGTTATTCCGTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagattgttacttacttgtgaagattctgtctgagggttttcgcgatttgtgtagGGAGAGTGAATCTAATAGGAGAGCACATCGATTACGAGGGTTATTCCGTGCTTCCAATGGCAATTCGCCAAGACACGGTGGTTGCTATCGGTAGGCGAGA
        tacttac  putative branch site (score: 1)
       ttactta  TA-rich tract